Starting phenix.real_space_refine on Sun Jul 21 20:28:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/07_2024/3j8a_6124_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/07_2024/3j8a_6124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/07_2024/3j8a_6124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/07_2024/3j8a_6124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/07_2024/3j8a_6124_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8a_6124/07_2024/3j8a_6124_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.038 sd= 1.493 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9925 2.51 5 N 2700 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 51": "OD1" <-> "OD2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 15800 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "G" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.65, per 1000 atoms: 0.55 Number of scatterers: 15800 At special positions: 0 Unit cell: (103.04, 97.44, 207.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 10 15.00 Mg 5 11.99 O 3060 8.00 N 2700 7.00 C 9925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.45 Conformation dependent library (CDL) restraints added in 2.5 seconds 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 0 sheets defined 52.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'F' and resid 97 through 231 removed outlier: 3.829A pdb=" N UNK F 129 " --> pdb=" O UNK F 125 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK F 143 " --> pdb=" O UNK F 139 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N UNK F 164 " --> pdb=" O UNK F 160 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N UNK F 170 " --> pdb=" O UNK F 166 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N UNK F 177 " --> pdb=" O UNK F 173 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK F 178 " --> pdb=" O UNK F 174 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK F 205 " --> pdb=" O UNK F 201 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N UNK F 209 " --> pdb=" O UNK F 205 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N UNK F 220 " --> pdb=" O UNK F 216 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N UNK F 223 " --> pdb=" O UNK F 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 231 removed outlier: 3.577A pdb=" N UNK G 123 " --> pdb=" O UNK G 119 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNK G 129 " --> pdb=" O UNK G 125 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N UNK G 143 " --> pdb=" O UNK G 139 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK G 164 " --> pdb=" O UNK G 160 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N UNK G 165 " --> pdb=" O UNK G 161 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N UNK G 198 " --> pdb=" O UNK G 194 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N UNK G 219 " --> pdb=" O UNK G 215 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNK G 226 " --> pdb=" O UNK G 222 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK G 227 " --> pdb=" O UNK G 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.613A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.888A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 141' Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.753A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.557A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 4.209A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 273 through 283 removed outlier: 3.922A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.507A pdb=" N LEU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.687A pdb=" N ILE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.577A pdb=" N ASP A 363 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.637A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.911A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.657A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 4.052A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.920A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.741A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.638A pdb=" N ILE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.562A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.768A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 141' Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 205 through 215 removed outlier: 3.711A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 removed outlier: 4.444A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C 229 " --> pdb=" O ASN C 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.994A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.509A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.542A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.756A pdb=" N ILE C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.683A pdb=" N ASP C 363 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.622A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 127 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.697A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 215 removed outlier: 3.959A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 removed outlier: 4.250A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 273 through 283 removed outlier: 3.909A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 310 through 321 removed outlier: 3.606A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.696A pdb=" N ILE D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 356 Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.691A pdb=" N ASP D 363 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.516A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 127 Processing helix chain 'E' and resid 137 through 141 removed outlier: 3.871A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 141' Processing helix chain 'E' and resid 182 through 194 removed outlier: 3.764A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 205 through 215 removed outlier: 3.728A pdb=" N VAL E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 removed outlier: 4.401A pdb=" N ALA E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 273 through 283 removed outlier: 3.816A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 310 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 removed outlier: 3.847A pdb=" N ILE E 345 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 356 Processing helix chain 'E' and resid 359 through 363 removed outlier: 3.705A pdb=" N ASP E 363 " --> pdb=" O GLN E 360 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 7.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5092 1.33 - 1.45: 2089 1.45 - 1.57: 8736 1.57 - 1.69: 16 1.69 - 1.81: 180 Bond restraints: 16113 Sorted by residual: bond pdb=" NE2 HIC A 73 " pdb=" CZ HIC A 73 " ideal model delta sigma weight residual 1.444 1.273 0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" NE2 HIC B 73 " pdb=" CZ HIC B 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" NE2 HIC D 73 " pdb=" CZ HIC D 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" NE2 HIC C 73 " pdb=" CZ HIC C 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" NE2 HIC E 73 " pdb=" CZ HIC E 73 " ideal model delta sigma weight residual 1.444 1.274 0.170 2.00e-02 2.50e+03 7.20e+01 ... (remaining 16108 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.92: 494 105.92 - 113.96: 9218 113.96 - 122.01: 8695 122.01 - 130.05: 3418 130.05 - 138.10: 109 Bond angle restraints: 21934 Sorted by residual: angle pdb=" C GLN E 263 " pdb=" N PRO E 264 " pdb=" CA PRO E 264 " ideal model delta sigma weight residual 119.84 109.99 9.85 1.25e+00 6.40e-01 6.21e+01 angle pdb=" N VAL E 201 " pdb=" CA VAL E 201 " pdb=" C VAL E 201 " ideal model delta sigma weight residual 110.62 118.31 -7.69 1.02e+00 9.61e-01 5.69e+01 angle pdb=" N LEU A 236 " pdb=" CA LEU A 236 " pdb=" C LEU A 236 " ideal model delta sigma weight residual 112.72 104.27 8.45 1.14e+00 7.69e-01 5.49e+01 angle pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" C VAL C 201 " ideal model delta sigma weight residual 110.62 117.99 -7.37 1.02e+00 9.61e-01 5.22e+01 angle pdb=" N LEU D 236 " pdb=" CA LEU D 236 " pdb=" C LEU D 236 " ideal model delta sigma weight residual 112.72 104.70 8.02 1.14e+00 7.69e-01 4.95e+01 ... (remaining 21929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.37: 8963 21.37 - 42.74: 579 42.74 - 64.11: 125 64.11 - 85.48: 1 85.48 - 106.85: 10 Dihedral angle restraints: 9678 sinusoidal: 3570 harmonic: 6108 Sorted by residual: dihedral pdb=" CA HIS C 101 " pdb=" C HIS C 101 " pdb=" N PRO C 102 " pdb=" CA PRO C 102 " ideal model delta harmonic sigma weight residual 180.00 151.71 28.29 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" O1B ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PB ADP C 402 " pdb=" PA ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 -166.86 106.85 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" O1B ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PB ADP E 402 " pdb=" PA ADP E 402 " ideal model delta sinusoidal sigma weight residual -60.00 -163.67 103.66 1 2.00e+01 2.50e-03 2.97e+01 ... (remaining 9675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1645 0.038 - 0.075: 522 0.075 - 0.113: 232 0.113 - 0.150: 90 0.150 - 0.188: 16 Chirality restraints: 2505 Sorted by residual: chirality pdb=" CA VAL B 54 " pdb=" N VAL B 54 " pdb=" C VAL B 54 " pdb=" CB VAL B 54 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA GLN E 263 " pdb=" N GLN E 263 " pdb=" C GLN E 263 " pdb=" CB GLN E 263 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA VAL D 54 " pdb=" N VAL D 54 " pdb=" C VAL D 54 " pdb=" CB VAL D 54 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 2502 not shown) Planarity restraints: 2828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 263 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" CD GLN A 263 " 0.050 2.00e-02 2.50e+03 pdb=" OE1 GLN A 263 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 GLN A 263 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 101 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO C 102 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 101 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO A 102 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.024 5.00e-02 4.00e+02 ... (remaining 2825 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 741 2.70 - 3.25: 16846 3.25 - 3.80: 24089 3.80 - 4.35: 32022 4.35 - 4.90: 49075 Nonbonded interactions: 122773 Sorted by model distance: nonbonded pdb=" OD2 ASP A 286 " pdb=" NH2 ARG C 39 " model vdw 2.145 2.520 nonbonded pdb=" OG SER B 52 " pdb=" NZ LYS B 84 " model vdw 2.153 2.520 nonbonded pdb=" OD2 ASP D 286 " pdb=" NH2 ARG E 39 " model vdw 2.169 2.520 nonbonded pdb=" O PRO C 332 " pdb=" NH1 ARG C 335 " model vdw 2.213 2.520 nonbonded pdb=" O LEU E 221 " pdb=" NZ LYS E 315 " model vdw 2.220 2.520 ... (remaining 122768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 41.160 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.171 16113 Z= 0.411 Angle : 1.270 13.096 21934 Z= 0.851 Chirality : 0.049 0.188 2505 Planarity : 0.005 0.047 2828 Dihedral : 14.877 106.855 5748 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 1.38 % Allowed : 11.22 % Favored : 87.40 % Rotamer: Outliers : 6.28 % Allowed : 15.08 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.31 (0.15), residues: 1810 helix: -4.21 (0.10), residues: 670 sheet: -2.64 (0.32), residues: 200 loop : -3.20 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.016 0.002 HIS C 275 PHE 0.016 0.002 PHE D 255 TYR 0.013 0.002 TYR A 169 ARG 0.005 0.001 ARG D 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 535 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9725 (OUTLIER) cc_final: 0.9510 (m) REVERT: A 10 CYS cc_start: 0.9116 (t) cc_final: 0.8704 (p) REVERT: A 100 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: A 111 ASN cc_start: 0.9228 (t0) cc_final: 0.9027 (t0) REVERT: A 123 MET cc_start: 0.8236 (ttt) cc_final: 0.8010 (ttp) REVERT: B 47 MET cc_start: 0.7148 (ptm) cc_final: 0.6928 (ptp) REVERT: B 100 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: B 132 MET cc_start: 0.8874 (tpp) cc_final: 0.8606 (tpt) REVERT: B 153 LEU cc_start: 0.9330 (tp) cc_final: 0.9105 (tp) REVERT: B 162 ASN cc_start: 0.9274 (t0) cc_final: 0.8757 (t0) REVERT: B 183 ARG cc_start: 0.9271 (mtt-85) cc_final: 0.8834 (ttm-80) REVERT: B 196 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8607 (mtt90) REVERT: B 199 SER cc_start: 0.9005 (p) cc_final: 0.8804 (p) REVERT: B 256 ARG cc_start: 0.9088 (ttp80) cc_final: 0.8771 (ttm-80) REVERT: B 334 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8452 (pt0) REVERT: B 337 TYR cc_start: 0.9183 (m-10) cc_final: 0.8952 (m-10) REVERT: B 345 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9192 (mt) REVERT: C 61 LYS cc_start: 0.9140 (mttt) cc_final: 0.8929 (mttt) REVERT: C 103 THR cc_start: 0.9462 (t) cc_final: 0.9253 (t) REVERT: C 111 ASN cc_start: 0.9108 (t0) cc_final: 0.8848 (t0) REVERT: C 121 GLN cc_start: 0.9326 (tt0) cc_final: 0.9117 (tm-30) REVERT: C 248 ILE cc_start: 0.9426 (mt) cc_final: 0.9128 (tt) REVERT: C 277 THR cc_start: 0.9439 (p) cc_final: 0.8960 (t) REVERT: C 325 MET cc_start: 0.9064 (tpp) cc_final: 0.8660 (tpt) REVERT: C 328 LYS cc_start: 0.8830 (mttt) cc_final: 0.8574 (mptt) REVERT: C 334 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: D 16 LEU cc_start: 0.9610 (mm) cc_final: 0.9406 (mp) REVERT: D 44 MET cc_start: 0.8567 (ttt) cc_final: 0.8085 (tmm) REVERT: D 115 ASN cc_start: 0.9107 (t0) cc_final: 0.8511 (t0) REVERT: D 132 MET cc_start: 0.8977 (tpp) cc_final: 0.8558 (mmm) REVERT: D 154 ASP cc_start: 0.8857 (t0) cc_final: 0.8523 (t0) REVERT: D 183 ARG cc_start: 0.9279 (mtt-85) cc_final: 0.8740 (tpp80) REVERT: D 213 LYS cc_start: 0.9555 (tttt) cc_final: 0.9221 (tttm) REVERT: D 316 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: D 336 LYS cc_start: 0.9428 (tttt) cc_final: 0.9202 (tttp) REVERT: D 340 TRP cc_start: 0.9250 (t60) cc_final: 0.8831 (t60) REVERT: D 345 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9258 (mt) REVERT: E 132 MET cc_start: 0.9093 (tpp) cc_final: 0.8847 (tpp) REVERT: E 167 GLU cc_start: 0.9056 (tt0) cc_final: 0.8816 (tm-30) REVERT: E 280 ASN cc_start: 0.9446 (t0) cc_final: 0.9238 (t0) REVERT: E 288 ASP cc_start: 0.9296 (t0) cc_final: 0.8998 (t0) REVERT: E 289 ILE cc_start: 0.9627 (OUTLIER) cc_final: 0.9349 (mm) REVERT: E 329 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9295 (mp) REVERT: E 334 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8674 (pt0) outliers start: 97 outliers final: 33 residues processed: 590 average time/residue: 0.2499 time to fit residues: 222.1333 Evaluate side-chains 467 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 422 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 30.0000 chunk 156 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 187 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 16113 Z= 0.292 Angle : 0.789 7.857 21934 Z= 0.402 Chirality : 0.045 0.173 2505 Planarity : 0.005 0.041 2828 Dihedral : 9.997 91.214 2421 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.63 % Favored : 92.54 % Rotamer: Outliers : 7.83 % Allowed : 20.91 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.17), residues: 1810 helix: -2.86 (0.16), residues: 645 sheet: -1.68 (0.40), residues: 150 loop : -2.30 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 340 HIS 0.013 0.002 HIS C 275 PHE 0.013 0.002 PHE D 255 TYR 0.017 0.001 TYR D 169 ARG 0.004 0.000 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 432 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9716 (OUTLIER) cc_final: 0.9503 (m) REVERT: A 10 CYS cc_start: 0.9075 (t) cc_final: 0.8665 (p) REVERT: A 39 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8656 (ptt180) REVERT: A 84 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8894 (ttpp) REVERT: A 237 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8748 (pt0) REVERT: A 242 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9066 (mp) REVERT: A 328 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8036 (mttp) REVERT: B 100 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: B 123 MET cc_start: 0.8340 (ttm) cc_final: 0.8131 (ttp) REVERT: B 133 TYR cc_start: 0.8937 (t80) cc_final: 0.8716 (t80) REVERT: B 162 ASN cc_start: 0.9122 (t0) cc_final: 0.8597 (t0) REVERT: B 329 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9072 (mm) REVERT: B 340 TRP cc_start: 0.8867 (t60) cc_final: 0.8183 (t60) REVERT: C 39 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8293 (ptt180) REVERT: C 121 GLN cc_start: 0.9321 (tm-30) cc_final: 0.9109 (tm-30) REVERT: C 248 ILE cc_start: 0.9381 (mt) cc_final: 0.9148 (tt) REVERT: C 259 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8849 (tm-30) REVERT: C 263 GLN cc_start: 0.9341 (tt0) cc_final: 0.9110 (tt0) REVERT: C 325 MET cc_start: 0.8901 (tpp) cc_final: 0.8544 (tpt) REVERT: C 328 LYS cc_start: 0.8619 (mttt) cc_final: 0.8220 (mptt) REVERT: D 16 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9368 (mp) REVERT: D 44 MET cc_start: 0.8777 (ttt) cc_final: 0.8546 (ttp) REVERT: D 100 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7941 (mm-30) REVERT: D 115 ASN cc_start: 0.9038 (t0) cc_final: 0.8670 (t0) REVERT: D 183 ARG cc_start: 0.9211 (mtt-85) cc_final: 0.8940 (tpp80) REVERT: D 242 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8997 (mp) REVERT: D 316 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: D 325 MET cc_start: 0.9188 (mmm) cc_final: 0.8555 (tpp) REVERT: D 334 GLU cc_start: 0.8618 (pt0) cc_final: 0.8386 (pt0) REVERT: D 340 TRP cc_start: 0.8943 (t60) cc_final: 0.8325 (t60) REVERT: E 39 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8066 (ptt180) REVERT: E 167 GLU cc_start: 0.9030 (tt0) cc_final: 0.8740 (tm-30) REVERT: E 289 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9252 (mm) outliers start: 121 outliers final: 61 residues processed: 505 average time/residue: 0.2359 time to fit residues: 181.4729 Evaluate side-chains 469 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 392 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 364 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 6.9990 chunk 58 optimal weight: 30.0000 chunk 155 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 51 optimal weight: 0.0870 chunk 187 optimal weight: 0.0050 chunk 202 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 185 optimal weight: 0.3980 chunk 63 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 overall best weight: 1.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16113 Z= 0.184 Angle : 0.718 9.004 21934 Z= 0.352 Chirality : 0.043 0.178 2505 Planarity : 0.004 0.038 2828 Dihedral : 9.165 82.338 2391 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.80 % Favored : 93.37 % Rotamer: Outliers : 6.67 % Allowed : 23.88 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.18), residues: 1810 helix: -2.32 (0.17), residues: 680 sheet: -2.82 (0.28), residues: 255 loop : -1.61 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 340 HIS 0.013 0.002 HIS C 275 PHE 0.010 0.001 PHE D 255 TYR 0.013 0.001 TYR D 169 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 429 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8896 (t) cc_final: 0.8668 (p) REVERT: A 39 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8591 (ptt180) REVERT: A 237 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8655 (pt0) REVERT: B 121 GLN cc_start: 0.9056 (tt0) cc_final: 0.8809 (tm-30) REVERT: B 124 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: B 154 ASP cc_start: 0.8357 (t0) cc_final: 0.7972 (t0) REVERT: B 162 ASN cc_start: 0.9060 (t0) cc_final: 0.8601 (t0) REVERT: B 329 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9083 (mm) REVERT: B 340 TRP cc_start: 0.8790 (t60) cc_final: 0.8205 (t60) REVERT: B 364 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8487 (pp20) REVERT: C 39 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8030 (ptt180) REVERT: C 259 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8935 (tm-30) REVERT: C 325 MET cc_start: 0.8822 (tpp) cc_final: 0.8447 (tpt) REVERT: C 359 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8942 (mtpp) REVERT: D 242 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8935 (mp) REVERT: D 334 GLU cc_start: 0.8534 (pt0) cc_final: 0.8224 (pt0) REVERT: E 39 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8023 (ptt180) REVERT: E 132 MET cc_start: 0.8873 (tpp) cc_final: 0.8596 (tpp) REVERT: E 167 GLU cc_start: 0.8957 (tt0) cc_final: 0.8696 (tm-30) REVERT: E 283 MET cc_start: 0.9010 (mtp) cc_final: 0.8712 (mtp) REVERT: E 289 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9047 (mm) outliers start: 103 outliers final: 54 residues processed: 487 average time/residue: 0.2369 time to fit residues: 175.2826 Evaluate side-chains 451 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 386 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 97 optimal weight: 0.0570 chunk 20 optimal weight: 100.0000 chunk 89 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 199 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16113 Z= 0.177 Angle : 0.693 9.890 21934 Z= 0.335 Chirality : 0.043 0.183 2505 Planarity : 0.004 0.037 2828 Dihedral : 8.547 77.020 2377 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.86 % Favored : 93.31 % Rotamer: Outliers : 7.51 % Allowed : 25.24 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.19), residues: 1810 helix: -1.97 (0.18), residues: 675 sheet: -2.35 (0.33), residues: 205 loop : -1.42 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 340 HIS 0.013 0.002 HIS C 275 PHE 0.012 0.001 PHE D 200 TYR 0.020 0.001 TYR D 169 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 412 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.8795 (t) cc_final: 0.8574 (p) REVERT: A 39 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8491 (ptt180) REVERT: B 44 MET cc_start: 0.8486 (ttp) cc_final: 0.8164 (ttm) REVERT: B 121 GLN cc_start: 0.9044 (tt0) cc_final: 0.8782 (tm-30) REVERT: B 124 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: B 154 ASP cc_start: 0.8283 (t0) cc_final: 0.7943 (t0) REVERT: B 162 ASN cc_start: 0.9006 (t0) cc_final: 0.8570 (t0) REVERT: B 329 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9094 (mm) REVERT: B 334 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: B 340 TRP cc_start: 0.8737 (t60) cc_final: 0.8319 (t60) REVERT: B 364 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8444 (pp20) REVERT: C 39 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8112 (ptt180) REVERT: C 259 GLU cc_start: 0.9347 (OUTLIER) cc_final: 0.9062 (tm-30) REVERT: C 325 MET cc_start: 0.8809 (tpp) cc_final: 0.8457 (tpt) REVERT: C 354 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8847 (mt0) REVERT: D 242 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8946 (mp) REVERT: D 325 MET cc_start: 0.8986 (mmm) cc_final: 0.8479 (tpp) REVERT: E 39 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7921 (ptt180) REVERT: E 132 MET cc_start: 0.9012 (tpp) cc_final: 0.8657 (tpp) REVERT: E 167 GLU cc_start: 0.8928 (tt0) cc_final: 0.8682 (tm-30) REVERT: E 189 LEU cc_start: 0.9593 (tp) cc_final: 0.9245 (tp) REVERT: E 275 HIS cc_start: 0.9444 (OUTLIER) cc_final: 0.8757 (p-80) REVERT: E 289 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9026 (mm) outliers start: 116 outliers final: 64 residues processed: 466 average time/residue: 0.2612 time to fit residues: 186.5073 Evaluate side-chains 461 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 385 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 2 optimal weight: 110.0000 chunk 148 optimal weight: 0.4980 chunk 82 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 0 optimal weight: 60.0000 chunk 101 optimal weight: 30.0000 chunk 178 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 275 HIS ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16113 Z= 0.163 Angle : 0.684 10.886 21934 Z= 0.326 Chirality : 0.043 0.162 2505 Planarity : 0.004 0.053 2828 Dihedral : 8.169 73.501 2377 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.83 % Allowed : 4.97 % Favored : 94.20 % Rotamer: Outliers : 6.99 % Allowed : 26.08 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.19), residues: 1810 helix: -1.69 (0.19), residues: 675 sheet: -2.21 (0.34), residues: 205 loop : -1.30 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 340 HIS 0.014 0.002 HIS C 275 PHE 0.013 0.001 PHE D 200 TYR 0.014 0.001 TYR D 169 ARG 0.003 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 414 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8451 (ptt180) REVERT: A 237 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8543 (pt0) REVERT: B 44 MET cc_start: 0.8403 (ttp) cc_final: 0.8147 (ttm) REVERT: B 100 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: B 121 GLN cc_start: 0.8986 (tt0) cc_final: 0.8706 (tm-30) REVERT: B 124 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: B 154 ASP cc_start: 0.8208 (t0) cc_final: 0.7788 (t0) REVERT: B 162 ASN cc_start: 0.8983 (t0) cc_final: 0.8586 (t0) REVERT: B 329 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9086 (mm) REVERT: B 364 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8638 (pp20) REVERT: C 39 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8075 (ptt180) REVERT: C 259 GLU cc_start: 0.9284 (tm-30) cc_final: 0.8721 (tm-30) REVERT: C 325 MET cc_start: 0.8774 (tpp) cc_final: 0.8430 (tpt) REVERT: D 124 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: D 242 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8892 (mp) REVERT: D 325 MET cc_start: 0.8916 (mmm) cc_final: 0.8398 (tpp) REVERT: E 39 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7869 (ptt180) REVERT: E 129 VAL cc_start: 0.8786 (t) cc_final: 0.8563 (p) REVERT: E 167 GLU cc_start: 0.8934 (tt0) cc_final: 0.8656 (tm-30) REVERT: E 275 HIS cc_start: 0.9365 (OUTLIER) cc_final: 0.8943 (p-80) REVERT: E 289 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8940 (mm) outliers start: 108 outliers final: 59 residues processed: 472 average time/residue: 0.2434 time to fit residues: 179.3276 Evaluate side-chains 464 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 393 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 8.9990 chunk 179 optimal weight: 20.0000 chunk 39 optimal weight: 0.0270 chunk 116 optimal weight: 6.9990 chunk 49 optimal weight: 0.1980 chunk 199 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 16 optimal weight: 60.0000 chunk 65 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.8444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN C 275 HIS ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16113 Z= 0.199 Angle : 0.684 9.263 21934 Z= 0.328 Chirality : 0.044 0.220 2505 Planarity : 0.004 0.038 2828 Dihedral : 7.606 71.512 2366 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.36 % Favored : 93.81 % Rotamer: Outliers : 6.86 % Allowed : 26.99 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.20), residues: 1810 helix: -1.55 (0.19), residues: 670 sheet: -2.12 (0.34), residues: 205 loop : -1.19 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 340 HIS 0.013 0.002 HIS C 275 PHE 0.013 0.001 PHE D 223 TYR 0.014 0.001 TYR D 169 ARG 0.004 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 407 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8497 (ptt180) REVERT: A 153 LEU cc_start: 0.9269 (tp) cc_final: 0.9022 (tp) REVERT: A 237 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8538 (pt0) REVERT: B 121 GLN cc_start: 0.8999 (tt0) cc_final: 0.8719 (tm-30) REVERT: B 124 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: B 154 ASP cc_start: 0.8188 (t0) cc_final: 0.7875 (t0) REVERT: B 162 ASN cc_start: 0.9011 (t0) cc_final: 0.8518 (t0) REVERT: B 299 MET cc_start: 0.8696 (mtm) cc_final: 0.8410 (mtm) REVERT: B 305 MET cc_start: 0.8841 (mmp) cc_final: 0.8631 (mmp) REVERT: B 329 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9084 (mm) REVERT: B 334 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: B 364 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8621 (pp20) REVERT: C 39 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8101 (ptt180) REVERT: C 259 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8778 (tm-30) REVERT: C 325 MET cc_start: 0.8779 (tpp) cc_final: 0.8447 (tpt) REVERT: D 47 MET cc_start: 0.7407 (ttp) cc_final: 0.7119 (mtp) REVERT: D 121 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8194 (tm-30) REVERT: D 124 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: D 242 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8870 (mp) REVERT: D 325 MET cc_start: 0.8916 (mmm) cc_final: 0.8374 (tpp) REVERT: E 39 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7980 (ptt180) REVERT: E 129 VAL cc_start: 0.8814 (t) cc_final: 0.8579 (p) REVERT: E 167 GLU cc_start: 0.8947 (tt0) cc_final: 0.8663 (tm-30) REVERT: E 275 HIS cc_start: 0.9388 (OUTLIER) cc_final: 0.9012 (p-80) REVERT: E 289 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8918 (mm) outliers start: 106 outliers final: 66 residues processed: 463 average time/residue: 0.2232 time to fit residues: 160.7222 Evaluate side-chains 466 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 388 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 7.9990 chunk 22 optimal weight: 90.0000 chunk 113 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 112 optimal weight: 0.0670 chunk 167 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 198 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 overall best weight: 4.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 16113 Z= 0.258 Angle : 0.691 8.682 21934 Z= 0.334 Chirality : 0.044 0.163 2505 Planarity : 0.004 0.057 2828 Dihedral : 7.311 71.826 2357 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.58 % Favored : 93.59 % Rotamer: Outliers : 7.25 % Allowed : 26.93 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.20), residues: 1810 helix: -1.53 (0.19), residues: 670 sheet: -2.10 (0.35), residues: 205 loop : -1.17 (0.22), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP A 340 HIS 0.013 0.002 HIS C 275 PHE 0.015 0.002 PHE D 223 TYR 0.014 0.001 TYR A 198 ARG 0.006 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 397 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8500 (ptt180) REVERT: A 153 LEU cc_start: 0.9292 (tp) cc_final: 0.9043 (tp) REVERT: A 237 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8544 (pt0) REVERT: B 121 GLN cc_start: 0.9043 (tt0) cc_final: 0.8742 (tm-30) REVERT: B 124 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: B 154 ASP cc_start: 0.8276 (t0) cc_final: 0.7841 (t0) REVERT: B 162 ASN cc_start: 0.9058 (t0) cc_final: 0.8504 (t0) REVERT: B 329 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9115 (mm) REVERT: B 334 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7365 (pm20) REVERT: B 340 TRP cc_start: 0.8348 (t60) cc_final: 0.7207 (t60) REVERT: B 364 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8593 (pp20) REVERT: C 39 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8097 (ptt180) REVERT: C 124 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: C 259 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8757 (tm-30) REVERT: C 283 MET cc_start: 0.9137 (tpp) cc_final: 0.8756 (mpp) REVERT: C 325 MET cc_start: 0.8768 (tpp) cc_final: 0.8452 (tpt) REVERT: D 124 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: D 190 MET cc_start: 0.9080 (tpp) cc_final: 0.8111 (ttt) REVERT: D 242 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8867 (mp) REVERT: D 275 HIS cc_start: 0.9471 (OUTLIER) cc_final: 0.9071 (p-80) REVERT: D 325 MET cc_start: 0.8974 (mmm) cc_final: 0.8455 (tpp) REVERT: E 39 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8057 (ptt180) REVERT: E 167 GLU cc_start: 0.8963 (tt0) cc_final: 0.8668 (tm-30) REVERT: E 275 HIS cc_start: 0.9436 (OUTLIER) cc_final: 0.9005 (p-80) REVERT: E 289 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8978 (mm) outliers start: 112 outliers final: 77 residues processed: 448 average time/residue: 0.2251 time to fit residues: 156.4847 Evaluate side-chains 474 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 383 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.0010 chunk 79 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 39 optimal weight: 0.0980 chunk 38 optimal weight: 0.0970 chunk 126 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 18 optimal weight: 120.0000 chunk 156 optimal weight: 4.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 16113 Z= 0.189 Angle : 0.689 9.647 21934 Z= 0.329 Chirality : 0.044 0.171 2505 Planarity : 0.004 0.037 2828 Dihedral : 7.167 69.990 2357 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.25 % Favored : 93.92 % Rotamer: Outliers : 6.28 % Allowed : 27.90 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.20), residues: 1810 helix: -1.40 (0.19), residues: 670 sheet: -1.95 (0.36), residues: 195 loop : -1.06 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP A 340 HIS 0.011 0.001 HIS C 275 PHE 0.012 0.001 PHE D 223 TYR 0.018 0.001 TYR A 198 ARG 0.003 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 403 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8478 (ptt180) REVERT: A 153 LEU cc_start: 0.9267 (tp) cc_final: 0.9030 (tp) REVERT: A 237 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8521 (pt0) REVERT: B 121 GLN cc_start: 0.9017 (tt0) cc_final: 0.8697 (tm-30) REVERT: B 124 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: B 154 ASP cc_start: 0.8159 (t0) cc_final: 0.7834 (t0) REVERT: B 162 ASN cc_start: 0.9029 (t0) cc_final: 0.8535 (t0) REVERT: B 329 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9024 (mm) REVERT: B 340 TRP cc_start: 0.8318 (t60) cc_final: 0.7268 (t60) REVERT: B 364 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8660 (pp20) REVERT: C 39 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8113 (ptt180) REVERT: C 124 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: C 238 LYS cc_start: 0.9029 (mttm) cc_final: 0.8712 (mttp) REVERT: C 259 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8764 (tm-30) REVERT: C 283 MET cc_start: 0.9114 (tpp) cc_final: 0.8727 (mpp) REVERT: C 325 MET cc_start: 0.8784 (tpp) cc_final: 0.8470 (tpt) REVERT: C 340 TRP cc_start: 0.8688 (t60) cc_final: 0.7769 (t60) REVERT: D 44 MET cc_start: 0.8929 (ttp) cc_final: 0.8685 (ttm) REVERT: D 47 MET cc_start: 0.7416 (ttp) cc_final: 0.7104 (mtp) REVERT: D 124 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: D 190 MET cc_start: 0.9062 (tpp) cc_final: 0.8036 (ttt) REVERT: D 242 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8842 (mp) REVERT: D 275 HIS cc_start: 0.9441 (OUTLIER) cc_final: 0.9117 (p-80) REVERT: D 325 MET cc_start: 0.8895 (mmm) cc_final: 0.8430 (tpp) REVERT: D 352 PHE cc_start: 0.9139 (p90) cc_final: 0.8828 (p90) REVERT: E 39 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7958 (ptt180) REVERT: E 167 GLU cc_start: 0.8934 (tt0) cc_final: 0.8641 (tm-30) REVERT: E 275 HIS cc_start: 0.9395 (OUTLIER) cc_final: 0.9017 (p-80) REVERT: E 289 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8901 (mm) outliers start: 97 outliers final: 68 residues processed: 451 average time/residue: 0.2262 time to fit residues: 157.6574 Evaluate side-chains 469 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 388 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 8.9990 chunk 190 optimal weight: 8.9990 chunk 173 optimal weight: 30.0000 chunk 185 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 167 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 16113 Z= 0.292 Angle : 0.721 9.652 21934 Z= 0.348 Chirality : 0.045 0.175 2505 Planarity : 0.005 0.069 2828 Dihedral : 7.352 70.603 2357 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.02 % Favored : 92.15 % Rotamer: Outliers : 6.34 % Allowed : 28.28 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.20), residues: 1810 helix: -1.36 (0.20), residues: 640 sheet: -2.09 (0.35), residues: 205 loop : -1.12 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.003 TRP A 340 HIS 0.011 0.002 HIS C 275 PHE 0.017 0.002 PHE C 255 TYR 0.034 0.001 TYR B 69 ARG 0.007 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 389 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8502 (ptt180) REVERT: A 153 LEU cc_start: 0.9312 (tp) cc_final: 0.9080 (tp) REVERT: A 237 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8532 (pt0) REVERT: B 124 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: B 154 ASP cc_start: 0.8289 (t0) cc_final: 0.8019 (t0) REVERT: B 162 ASN cc_start: 0.9063 (t0) cc_final: 0.8507 (t0) REVERT: B 283 MET cc_start: 0.8941 (mtp) cc_final: 0.8689 (mtt) REVERT: B 329 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9060 (mm) REVERT: B 340 TRP cc_start: 0.8416 (t60) cc_final: 0.7501 (t60) REVERT: B 364 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: C 39 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8171 (ptt180) REVERT: C 124 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: C 259 GLU cc_start: 0.9310 (tm-30) cc_final: 0.8960 (tm-30) REVERT: C 283 MET cc_start: 0.9191 (tpp) cc_final: 0.8794 (mpp) REVERT: C 325 MET cc_start: 0.8772 (tpp) cc_final: 0.8492 (tpt) REVERT: D 47 MET cc_start: 0.7600 (ttp) cc_final: 0.7277 (mtp) REVERT: D 124 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: D 190 MET cc_start: 0.9008 (tpp) cc_final: 0.8067 (ttt) REVERT: D 242 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8870 (mp) REVERT: D 275 HIS cc_start: 0.9505 (OUTLIER) cc_final: 0.9198 (p-80) REVERT: D 325 MET cc_start: 0.9023 (mmm) cc_final: 0.8485 (tpp) REVERT: E 39 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8100 (ptt180) REVERT: E 167 GLU cc_start: 0.8962 (tt0) cc_final: 0.8664 (tm-30) REVERT: E 275 HIS cc_start: 0.9463 (OUTLIER) cc_final: 0.9055 (p-80) REVERT: E 289 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9024 (mm) REVERT: E 325 MET cc_start: 0.8577 (tpt) cc_final: 0.8195 (tpt) outliers start: 98 outliers final: 69 residues processed: 439 average time/residue: 0.2255 time to fit residues: 153.2301 Evaluate side-chains 459 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 377 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 0.0670 chunk 195 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 188 optimal weight: 0.4980 chunk 163 optimal weight: 6.9990 chunk 16 optimal weight: 80.0000 chunk 126 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 overall best weight: 2.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16113 Z= 0.199 Angle : 0.713 9.820 21934 Z= 0.343 Chirality : 0.045 0.319 2505 Planarity : 0.004 0.042 2828 Dihedral : 7.252 69.709 2357 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.64 % Favored : 93.54 % Rotamer: Outliers : 5.57 % Allowed : 29.32 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1810 helix: -1.31 (0.20), residues: 640 sheet: -2.07 (0.34), residues: 205 loop : -1.06 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.003 TRP A 340 HIS 0.011 0.001 HIS C 275 PHE 0.014 0.001 PHE D 200 TYR 0.018 0.001 TYR C 133 ARG 0.004 0.000 ARG A 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 400 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8474 (ptt180) REVERT: A 124 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: A 153 LEU cc_start: 0.9264 (tp) cc_final: 0.9049 (tp) REVERT: A 237 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8544 (pt0) REVERT: A 352 PHE cc_start: 0.9092 (p90) cc_final: 0.8766 (p90) REVERT: B 121 GLN cc_start: 0.9007 (tt0) cc_final: 0.8671 (tm-30) REVERT: B 124 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: B 154 ASP cc_start: 0.8243 (t0) cc_final: 0.7847 (t0) REVERT: B 162 ASN cc_start: 0.9037 (t0) cc_final: 0.8527 (t0) REVERT: B 283 MET cc_start: 0.8915 (mtp) cc_final: 0.8599 (mtt) REVERT: B 329 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9011 (mm) REVERT: B 340 TRP cc_start: 0.8327 (t60) cc_final: 0.7342 (t60) REVERT: B 364 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: C 39 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8090 (ptt180) REVERT: C 124 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: C 283 MET cc_start: 0.9157 (tpp) cc_final: 0.8768 (mpp) REVERT: C 325 MET cc_start: 0.8759 (tpp) cc_final: 0.8449 (tpt) REVERT: C 340 TRP cc_start: 0.8737 (t60) cc_final: 0.7798 (t60) REVERT: D 124 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: D 190 MET cc_start: 0.9011 (tpp) cc_final: 0.8163 (ttt) REVERT: D 242 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8846 (mp) REVERT: D 275 HIS cc_start: 0.9478 (OUTLIER) cc_final: 0.9231 (p-80) REVERT: D 325 MET cc_start: 0.8969 (mmm) cc_final: 0.8452 (tpp) REVERT: D 352 PHE cc_start: 0.9149 (p90) cc_final: 0.8846 (p90) REVERT: E 39 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7983 (ptt180) REVERT: E 167 GLU cc_start: 0.8937 (tt0) cc_final: 0.8647 (tm-30) REVERT: E 275 HIS cc_start: 0.9451 (OUTLIER) cc_final: 0.9088 (p-80) REVERT: E 289 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8896 (mm) outliers start: 86 outliers final: 69 residues processed: 447 average time/residue: 0.2264 time to fit residues: 157.7756 Evaluate side-chains 475 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 392 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 24 optimal weight: 110.0000 chunk 45 optimal weight: 20.0000 chunk 163 optimal weight: 30.0000 chunk 68 optimal weight: 10.0000 chunk 168 optimal weight: 20.0000 chunk 20 optimal weight: 110.0000 chunk 30 optimal weight: 5.9990 overall best weight: 6.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101456 restraints weight = 32546.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.104028 restraints weight = 15388.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105993 restraints weight = 8637.054| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 16113 Z= 0.333 Angle : 0.748 9.739 21934 Z= 0.363 Chirality : 0.047 0.329 2505 Planarity : 0.005 0.041 2828 Dihedral : 7.465 70.655 2357 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.73 % Favored : 91.44 % Rotamer: Outliers : 6.02 % Allowed : 29.06 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 2.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.20), residues: 1810 helix: -1.43 (0.20), residues: 640 sheet: -2.17 (0.35), residues: 205 loop : -1.16 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.104 0.003 TRP A 340 HIS 0.012 0.002 HIS C 275 PHE 0.022 0.002 PHE D 200 TYR 0.019 0.001 TYR C 133 ARG 0.005 0.000 ARG C 290 =============================================================================== Job complete usr+sys time: 3574.53 seconds wall clock time: 64 minutes 39.92 seconds (3879.92 seconds total)